SARS-CoV-2 Variants Research and Vaccines

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Vaccines and Therapeutic Developments".

Deadline for manuscript submissions: closed (20 November 2023) | Viewed by 10325

Special Issue Editors


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Guest Editor
Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
Interests: COVID-19 therapeutics; natural therapies; liver cancer and molecular biomarkers for COVID-19 and liver cancer

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Guest Editor
RESPIRE Clinical Research, Palm Springs, CA 92262, USA
Interests: COVID; pulmonary hypertension; idiopathic pulmonary fibrosis; non-tuberculous mycobacteria; COPD

Special Issue Information

Dear Colleagues,

Over the span of more than two years since the beginning of the COVID-19 pandemic, the world has witnessed the evolution of the virus through different variants which have affected global communities in many different ways to the original virus. These variants have also caused different symptoms and differences in the make-up of the infected individuals. In addition to breakthroughs in therapeutic and preventive medicine driven by the pandemic, practices have had to adapt to new ways of medicine delivery, and researchers have toiled to chronicle the layers of social, economic, and political consequences of the pandemic.

As we await the endemicity of COVID-19, waves of new variants are producing new symptoms and making multiple treatments, which were thought to be lifesaving in their inception, obsolete. Clinical trials must anticipate the future landscape that is likely to exist when they are able to be implemented in an ever-changing patient profile and attitude towards research.

This Special Issue, which is dedicated to COVID-19 two years on, will consider submissions regarding topics such as prognostic indicators of COVID-19 infections, the global heterogeneity of patients affected by local variants of the SARS-CoV2 virus, the evolving approaches to diagnosis, treatment, and prevention (including masks and vaccines), along with future directions in these respective themes.

Areas of specific interest include:

  1. The natural course of COVID-19 infection along with outcome-based tools to classify the severity of infections.
  2. Prognostic indicators of the progression of mild–moderate COVID-19 infection to severe infection and death.
  3. Therapeutic approaches to COVID-19 infection based on its severity, including outpatient versus inpatient settings.
  4. Prognostic indicators of morbidity and mortality in COVID-19 infection.
  5. Definition and pathogenesis of long COVID symptoms post COVID-19 infection.
  6. COVID-19 severity and mortality rates based on ethnicity, age, gender, socio-economic status, and geographic location.
  7. COVID-19 variants and their responses to vaccines.
  8. The impact and longevity of the immunogenic response of vaccines in various patient populations.

This Special Issue reflects the unprecedented unity of researchers that has been witnessed globally in the face of a common threat to humanity and aims to feature the brightest discoveries in this field. 

Prof. Dr. Ahmed O. Kaseb
Dr. Hassan Bencheqroun
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • COVID-19 infection
  • COVID antiviral
  • SARS antigen test
  • SARS RT-PCR
  • COVID-19 treatment
  • vaccination
  • long COVID

Published Papers (5 papers)

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Research

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14 pages, 4289 KiB  
Article
Computational Investigation of Selected Spike Protein Mutations in SARS-CoV-2: Delta, Omicron, and Some Circulating Subvariants
by Urmi Roy
Pathogens 2024, 13(1), 10; https://doi.org/10.3390/pathogens13010010 - 21 Dec 2023
Viewed by 1192
Abstract
Among the multiple SARS-CoV-2 variants recently reported, the Delta variant has generated the most perilous and widespread effects. Another variant, Omicron, has been identified specifically for its high transmissibility. Omicron contains numerous spike (S) protein mutations and numbers much larger than those of [...] Read more.
Among the multiple SARS-CoV-2 variants recently reported, the Delta variant has generated the most perilous and widespread effects. Another variant, Omicron, has been identified specifically for its high transmissibility. Omicron contains numerous spike (S) protein mutations and numbers much larger than those of its predecessor variants. In this report, the author has discussed some essential structural aspects and time-based structure changes of a selected set of spike protein mutations within the Delta and Omicron variants. The expected impact of multiple point mutations within the spike protein’s receptor-binding domain (RBD) and S1 of these variants are examined. Additionally, the RBDs of the more recently emerged subvariants BA.4, BA.5, and BA.2.12.1 are discussed. Within the latter group, BA.5 represents the most prevalent form of SARS-CoV-2 globally until recently. This computational work also briefly explores the temporal mutation profile for the currently circulating variants of interest (VOIs), variants under monitoring (VUMs), and variants being monitored (VBMs) including XBB.1.5, BQ.1, BA.2.75, CH.1.1, XBB, XBF, EG.5 (or Eris), and BA.2.86 (or Pirola). It is expected that these structural data can facilitate the tasks of identifying drug targets and neutralizing antibodies for the evolving variants/subvariants of SARS-CoV-2. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants Research and Vaccines)
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14 pages, 816 KiB  
Article
Evolving Clinical Manifestations and Outcomes in COVID-19 Patients: A Comparative Analysis of SARS-CoV-2 Variant Waves in a Romanian Hospital Setting
by Violeta Briciu, Daniel-Corneliu Leucuta, Monica Muntean, Amanda Radulescu, Cristina Cismaru, Adriana Topan, Lucia Herbel, Melinda Horvat, Mihai Calin, Roxana Dobrota and Mihaela Lupse
Pathogens 2023, 12(12), 1453; https://doi.org/10.3390/pathogens12121453 - 14 Dec 2023
Cited by 1 | Viewed by 1123
Abstract
The aim of this study was to evaluate differences in the clinical manifestations and outcomes in hospitalized patients with COVID-19 in a single Romanian center during four pandemic waves determined by different SARS-CoV-2 variants of concern (VOCs). A retrospective study on 9049 consecutive [...] Read more.
The aim of this study was to evaluate differences in the clinical manifestations and outcomes in hospitalized patients with COVID-19 in a single Romanian center during four pandemic waves determined by different SARS-CoV-2 variants of concern (VOCs). A retrospective study on 9049 consecutive hospitalized adult patients was performed between 27 February 2020 and 31 March 2023. The study interval was divided into waves based on national data on SARS-CoV-2 VOCs’ circulation. Multivariate logistic regression models were built, predicting death and complications as functions of comorbidities, therapy, wave, severity form, and vaccination status, and adjusted for ages ≥65 years. Pulmonary (pneumothorax/pneumomediastinum, pulmonary embolism) and extrapulmonary complications (liver injury, acute kidney injury, ischemic/hemorrhagic stroke, myocardial infarction, and gastrointestinal bleeding) were present, more frequently in ICU hospitalized patients and with differences between waves. The highest in-hospital mortality was found in patients presenting pneumothorax/pneumomediastinum. All of the evaluated risk factors were significantly associated with death, except for obesity and the Omicron wave. Our study highlights the changing nature of COVID-19 and acknowledges the impacts of viral mutations on disease outcomes. For all four waves, COVID-19 was a severe disease with a high risk of poor outcomes. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants Research and Vaccines)
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19 pages, 1731 KiB  
Article
SARS-CoV-2 Prevalence on and Incidence after Arrival in Travelers on Direct Flights from Cape Town, South Africa to Munich, Germany Shortly after Occurrence of the Omicron Variant in November/December 2021: Results from the OMTRAIR Study
by Cornelia Seidl, Liza Coyer, Nikolaus Ackermann, Katharina Katz, Jan Walter, Siegfried Ippisch, Martin Hoch and Merle M. Böhmer
Pathogens 2023, 12(2), 354; https://doi.org/10.3390/pathogens12020354 - 20 Feb 2023
Viewed by 2065
Abstract
The highly transmissible SARS-CoV-2-variant B.1.1.529 (Omicron) first appeared in South Africa in November 2021. In order to study Omicron entry to Germany, its occurrence related to incoming airline travel, symptomatology and compliance with entry regulations and recommendations, we conducted a cross-sectional study, followed [...] Read more.
The highly transmissible SARS-CoV-2-variant B.1.1.529 (Omicron) first appeared in South Africa in November 2021. In order to study Omicron entry to Germany, its occurrence related to incoming airline travel, symptomatology and compliance with entry regulations and recommendations, we conducted a cross-sectional study, followed by a retrospective cohort study among passengers and crew on 19 direct flights from Cape Town, South Africa, to Munich, Germany, between 26 November and 23 December 2021. Travelers were mandatorily PCR-tested on arrival and invited to complete an online questionnaire. SARS-CoV-2-prevalence on arrival was 3.3% (n = 90/2728), and 93% were Omicron. Of the passengers, 528 (19%) completed the questionnaire. Among participants who tested negative on arrival, self-reported SARS-CoV-2-incidence was 4.3% within 14 days, of whom 74% reported a negative PCR-test ≤ 48 h before boarding, 77% were fully vaccinated, and 90% reported wearing an FFP2/medical mask during flight. We found multiple associations between risk factors and infection on and after arrival, among which having a positive-tested travel partner was the most noteworthy. In conclusion, PCR testing before departure was insufficient to control the introduction of the Omicron variant. Additional measures (e.g., frequent testing, quarantine after arrival or travel ban) should be considered to delay virus introduction in such settings. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants Research and Vaccines)
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13 pages, 1127 KiB  
Article
Host tRNA-Derived RNAs Target the 3′Untranslated Region of SARS-CoV-2
by Emily N. Hendrickson, Marna E. Ericson and Lynne T. Bemis
Pathogens 2022, 11(12), 1479; https://doi.org/10.3390/pathogens11121479 - 06 Dec 2022
Viewed by 1313
Abstract
The COVID-19 pandemic revealed a need for new understanding of the mechanisms regulating host–pathogen interactions during viral infection. Transfer RNA-derived RNAs (tDRs), previously called transfer RNA fragments (tRFs), have recently emerged as potential regulators of viral pathogenesis. Many predictive studies using bioinformatic approaches [...] Read more.
The COVID-19 pandemic revealed a need for new understanding of the mechanisms regulating host–pathogen interactions during viral infection. Transfer RNA-derived RNAs (tDRs), previously called transfer RNA fragments (tRFs), have recently emerged as potential regulators of viral pathogenesis. Many predictive studies using bioinformatic approaches have been conducted providing a repertoire of potential small RNA candidates for further analyses; however, few targets have been validated to directly bind to SARS-CoV-2 sequences. In this study, we used available data sets to identify host tDR expression altered in response to SARS-CoV-2 infection. RNA-interaction-prediction tools were used to identify sequences in the SARS-CoV-2 genome where tDRs could potentially bind. We then developed luciferase assays to confirm direct regulation through a predicted region of SARS-CoV-2 by tDRs. We found that two tDRs were downregulated in both clinical and in vitro cell culture studies of SARS-CoV-2 infection. Binding sites for these two tDRs were present in the 3′ untranslated region (3′UTR) of the SARS-CoV-2 reference virus and both sites were altered in Variants of Concern (VOCs) that emerged later in the pandemic. These studies directly confirm the binding of human tDRs to a specific region of the 3′UTR of SARS-CoV-2 providing evidence for a novel mechanism for host–pathogen regulation. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants Research and Vaccines)
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Review

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13 pages, 805 KiB  
Review
COVID-19 Vaccination and Alcohol Consumption: Justification of Risks
by Pavel A. Solopov
Pathogens 2023, 12(2), 163; https://doi.org/10.3390/pathogens12020163 - 19 Jan 2023
Cited by 4 | Viewed by 4035
Abstract
Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, pharmaceutical companies and research institutions have been actively working to develop vaccines, and the mass roll-out of vaccinations against COVID-19 began in January 2021. At the same time, during lockdowns, [...] Read more.
Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, pharmaceutical companies and research institutions have been actively working to develop vaccines, and the mass roll-out of vaccinations against COVID-19 began in January 2021. At the same time, during lockdowns, the consumption of alcoholic beverages increased. During the peak of vaccination, consumption remained at high levels around the world, despite the gradual relaxation of quarantine restrictions. Two of the popular queries on search engines were whether it is safe to drink alcohol after vaccination and whether this will affect the effectiveness of vaccines. Over the past two years, many studies have been published suggesting that excessive drinking not only worsens the course of an acute respiratory distress syndrome caused by the SARS-CoV-2 virus but can also exacerbate post-COVID-19 syndrome. Despite all sorts of online speculation, there is no specific scientific data on alcohol-induced complications after vaccination in the literature. Most of the published vaccine clinical trials do not include groups of patients with a history of alcohol-use disorders. This review analyzed the well-known and new mechanisms of action of COVID-19 vaccines on the immune system and the effects of alcohol and its metabolites on these mechanisms. Full article
(This article belongs to the Special Issue SARS-CoV-2 Variants Research and Vaccines)
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